jdalapicolla / langen_pipeline_version2 Goto Github PK

Hello there,
first all, thank you very much Jeronymo for the huge work and for putting these scripts online.
I was doing some analyses with a ddRAD seq database I have and I was at point #8 ("TESTING THE MISSING DATA INFLUENCE ON GENETIC STRUCTURE") of "1.1_FILTERING_SNPs". However, as I tried to do the PCA, I got the following error:

Error in file(file, ifelse(append, "a", "w")) : cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) : cannot open file 'Results_Filters/PCA/Axis_coord_test_chordo_Adapative_all_20_PC.csv': No such file or directory
("chordo" is the name of the project)
Checking on the codes, I did not notice the all_20_PC.csv file and when it should be generated.
I followed the code basically as written, script-by-script, just changing the R2 value when calculating LD.

It has to be noticed that everything goes well until that point. I honestly have no idea of what I could miss. Therefore, what could be the cause of this error?
Thanks in advance for the answer and sorry for the bother

Hello Ph.D Jeronymo，
Thanks very much for your code. I'm a beginner in bioinformatics. When I was studying your script, I couldn't find the file "functions_LanGen.R" .Can you tell me where it is?

Hello Jeronymo,

I am at this chunk of code, using tess3 method to do spatial genetic structuring.

at the line 905, which "project" object do you mean? Maybe you mean the best run object called "res" at line 895?

Thanks,

Hello Jeronymo, Thanks for your help along the way.

Whenever I rerun the tess3 function, I receive a different qmatrix, and result in different ancestry proportions for my barplot. Why is it so? Should I do the "set.seed()?"

I adapted your code and took out the loop and lambda parameter.

`K = c(1:5) # set the number of K to be tested
ploidy = 2 # species ploidy
CPU = 4 #Number of cores for run in parallel

tess3.ls <- tess3(X = genotypes, coord = coordinates, K = K,
method = "projected.ls", ploidy = ploidy, openMP.core.num = CPU)

q.matrix <- qmatrix(tess3.ls, K = 5)

my.colors <- c(1:5)
my.palette <- CreatePalette(my.colors, 6)
barplot(q.matrix, border = T, space = 0,
main = "Ancestry matrix",
xlab = "Individuals", ylab = "Ancestry proportions",
col.palette = my.palette) -> bp
axis(1, at = 0.5:nrow(q.matrix), labels = snps@meta[,3][bp$order], las = 3, cex.axis = 1)
`

Hello Jeronymo. Thank you for your previous help.

How did you determine this r2 value? I couldn't find it in the code. Can you share a resource or tutorial ?